EHV-1 Canonic Transcript dynamics (TSS ~ TES)
Balázs Kakuk
## Error in read.table(file = file, header = header, sep = sep, quote = quote, :
## object 'config' not foundProject info
Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)
Canonic Transcript dynamics (TSS ~ TES)
Those reads were counted only, where both the 3-prime AND the 5-prime adapters were “correct” (according to LoRTIA)
When counting with either adapters, the clustering grouped ORF64 together with two late genes
Statistics of counts
Difference from mean
Varcoeff
Clustering of samples
## Bootstrap (r = 0.5)... Done.## Bootstrap (r = 0.59)... Done.## Bootstrap (r = 0.7)... Done.## Bootstrap (r = 0.79)... Done.## Bootstrap (r = 0.89)... Done.## Bootstrap (r = 1.0)... Done.## Bootstrap (r = 1.09)... Done.## Bootstrap (r = 1.2)... Done.## Bootstrap (r = 1.29)... Done.## Bootstrap (r = 1.39)... Done.
The sample 48h_3 stands out!
Filtering of samples
Clustering of genes into de-novo clusters using hierarchial clustering
Cluster memberships
## Bootstrap (r = 0.5)... Done.## Bootstrap (r = 0.58)... Done.## Bootstrap (r = 0.69)... Done.## Bootstrap (r = 0.77)... Done.## Bootstrap (r = 0.88)... Done.## Bootstrap (r = 1.0)... Done.## Bootstrap (r = 1.08)... Done.## Bootstrap (r = 1.19)... Done.## Bootstrap (r = 1.27)... Done.## Bootstrap (r = 1.38)... Done.Optimal number of clusters
Find the optimal number of clusters to cut the tree at and calculate
Clustering statistics: Cluster number: 5
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 2: 1 ORF2 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 3: 1 ORF3 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 4: 1 ORF4 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 5: 1 ORF8 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 6: 1 ORF9 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 7: 1 ORF11 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 8: 1 ORF14 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 9: 1 ORF18 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 10: 1 ORF19 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 11: 1 ORF20 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 12: 1 ORF21 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 13: 1 ORF22 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 14: 1 ORF23 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 15: 1 ORF24 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 16: 1 ORF25 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 17: 1 ORF26 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 18: 1 ORF28 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 19: 1 ORF29 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 20: 1 ORF31 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 21: 1 ORF33 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 22: 1 ORF34 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 23: 1 ORF35.5 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 24: 1 ORF36 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 25: 1 ORF37 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 26: 1 ORF38 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 27: 1 ORF39 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 28: 1 CTO 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 29: 1 ORF40 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 30: 1 ORF42 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 31: 1 ORF43 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 32: 1 ORF44 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 33: 1 ORF46 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 34: 1 ORF49 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 35: 1 ORF50 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 36: 1 ORF51 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 37: 1 ORF58 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 38: 1 ORF61 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 39: 1 ORF62 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 40: 1 ORF64_1 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 41: 1 ORF66_1 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 42: 1 ORF68 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 43: 1 ORF73 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 44: 1 ORF74 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 45: 1 ORF75 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 46: 1 ORF76 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 47: 2 ORF5 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 48: 2 ORF7 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 49: 2 ORF10 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 50: 2 ORF17 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 51: 2 ORF30 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 52: 2 ORF53 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 53: 2 ORF63 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 54: 2 NOIR_2 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 55: 3 ORF6 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 56: 3 ORF65_1 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 57: 3 ORF67_1 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 58: 4 ORF12 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 59: 4 ORF13 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 60: 4 ORF15 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 61: 4 ORF16 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 62: 4 ORF27 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 63: 4 ORF32 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 64: 4 ORF35 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 65: 4 ORF41 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 66: 4 ORF48 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 67: 4 ORF52 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 68: 4 ORF54 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 69: 4 ORF57 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 70: 4 ORF59 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 71: 4 ORF60 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 72: 4 NOIR_1 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 73: 4 ORF71 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 74: 4 ORF72 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 75: 5 ORF69 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 76: 5 ORF70 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.002462135 -2.7431302 0.9996434 0.111936808
## 2: 0.002462135 -2.7431302 0.9996434 0.111936808
## 3: 0.002462135 -2.7431302 0.9996434 0.111936808
## 4: 0.002462135 -2.7431302 0.9996434 0.111936808
## 5: 0.002462135 -2.7431302 0.9996434 0.111936808
## 6: 0.002462135 -2.7431302 0.9996434 0.111936808
## 7: 0.002462135 -2.7431302 0.9996434 0.111936808
## 8: 0.002462135 -2.7431302 0.9996434 0.111936808
## 9: 0.002462135 -2.7431302 0.9996434 0.111936808
## 10: 0.002462135 -2.7431302 0.9996434 0.111936808
## 11: 0.002462135 -2.7431302 0.9996434 0.111936808
## 12: 0.002462135 -2.7431302 0.9996434 0.111936808
## 13: 0.002462135 -2.7431302 0.9996434 0.111936808
## 14: 0.002462135 -2.7431302 0.9996434 0.111936808
## 15: 0.002462135 -2.7431302 0.9996434 0.111936808
## 16: 0.002462135 -2.7431302 0.9996434 0.111936808
## 17: 0.002462135 -2.7431302 0.9996434 0.111936808
## 18: 0.002462135 -2.7431302 0.9996434 0.111936808
## 19: 0.002462135 -2.7431302 0.9996434 0.111936808
## 20: 0.002462135 -2.7431302 0.9996434 0.111936808
## 21: 0.002462135 -2.7431302 0.9996434 0.111936808
## 22: 0.002462135 -2.7431302 0.9996434 0.111936808
## 23: 0.002462135 -2.7431302 0.9996434 0.111936808
## 24: 0.002462135 -2.7431302 0.9996434 0.111936808
## 25: 0.002462135 -2.7431302 0.9996434 0.111936808
## 26: 0.002462135 -2.7431302 0.9996434 0.111936808
## 27: 0.002462135 -2.7431302 0.9996434 0.111936808
## 28: 0.002462135 -2.7431302 0.9996434 0.111936808
## 29: 0.002462135 -2.7431302 0.9996434 0.111936808
## 30: 0.002462135 -2.7431302 0.9996434 0.111936808
## 31: 0.002462135 -2.7431302 0.9996434 0.111936808
## 32: 0.002462135 -2.7431302 0.9996434 0.111936808
## 33: 0.002462135 -2.7431302 0.9996434 0.111936808
## 34: 0.002462135 -2.7431302 0.9996434 0.111936808
## 35: 0.002462135 -2.7431302 0.9996434 0.111936808
## 36: 0.002462135 -2.7431302 0.9996434 0.111936808
## 37: 0.002462135 -2.7431302 0.9996434 0.111936808
## 38: 0.002462135 -2.7431302 0.9996434 0.111936808
## 39: 0.002462135 -2.7431302 0.9996434 0.111936808
## 40: 0.002462135 -2.7431302 0.9996434 0.111936808
## 41: 0.002462135 -2.7431302 0.9996434 0.111936808
## 42: 0.002462135 -2.7431302 0.9996434 0.111936808
## 43: 0.002462135 -2.7431302 0.9996434 0.111936808
## 44: 0.002462135 -2.7431302 0.9996434 0.111936808
## 45: 0.002462135 -2.7431302 0.9996434 0.111936808
## 46: 0.002462135 -2.7431302 0.9996434 0.111936808
## 47: 0.004791635 -1.4740665 0.8338440 0.032372715
## 48: 0.004791635 -1.4740665 0.8338440 0.032372715
## 49: 0.004791635 -1.4740665 0.8338440 0.032372715
## 50: 0.004791635 -1.4740665 0.8338440 0.032372715
## 51: 0.004791635 -1.4740665 0.8338440 0.032372715
## 52: 0.004791635 -1.4740665 0.8338440 0.032372715
## 53: 0.004791635 -1.4740665 0.8338440 0.032372715
## 54: 0.004791635 -1.4740665 0.8338440 0.032372715
## 55: 0.003807918 -2.3395432 1.1685483 0.376504068
## 56: 0.003807918 -2.3395432 1.1685483 0.376504068
## 57: 0.003807918 -2.3395432 1.1685483 0.376504068
## 58: 0.004535461 -1.6400338 0.8477994 0.110459671
## 59: 0.004535461 -1.6400338 0.8477994 0.110459671
## 60: 0.004535461 -1.6400338 0.8477994 0.110459671
## 61: 0.004535461 -1.6400338 0.8477994 0.110459671
## 62: 0.004535461 -1.6400338 0.8477994 0.110459671
## 63: 0.004535461 -1.6400338 0.8477994 0.110459671
## 64: 0.004535461 -1.6400338 0.8477994 0.110459671
## 65: 0.004535461 -1.6400338 0.8477994 0.110459671
## 66: 0.004535461 -1.6400338 0.8477994 0.110459671
## 67: 0.004535461 -1.6400338 0.8477994 0.110459671
## 68: 0.004535461 -1.6400338 0.8477994 0.110459671
## 69: 0.004535461 -1.6400338 0.8477994 0.110459671
## 70: 0.004535461 -1.6400338 0.8477994 0.110459671
## 71: 0.004535461 -1.6400338 0.8477994 0.110459671
## 72: 0.004535461 -1.6400338 0.8477994 0.110459671
## 73: 0.004535461 -1.6400338 0.8477994 0.110459671
## 74: 0.004535461 -1.6400338 0.8477994 0.110459671
## 75: 0.005045937 -0.7647494 0.3581624 0.003891377
## 76: 0.005045937 -0.7647494 0.3581624 0.003891377
## se.bp v c pchi
## [1] "ORF44" "ORF58" "ORF25" "ORF35.5" "ORF64_1" "ORF50" "ORF42"
## [8] "ORF33" "ORF34" "ORF62" "ORF4" "ORF20" "ORF21" "ORF61"
## [15] "ORF31" "ORF1" "NOIR_1" "ORF32" "ORF59" "ORF69"## [1] 20## [1] "ORF69" "ORF70"## [1] 2Clustering statistics: Cluster number: 6
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 2: 1 ORF4 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 3: 1 ORF9 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 4: 1 ORF19 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 5: 1 ORF20 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 6: 1 ORF21 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 7: 1 ORF31 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 8: 1 ORF34 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 9: 1 ORF37 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 10: 1 ORF38 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 11: 1 ORF49 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 12: 1 ORF50 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 13: 1 ORF51 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 14: 1 ORF61 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 15: 1 ORF64_1 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 16: 2 ORF2 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 17: 2 ORF3 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 18: 2 ORF8 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 19: 2 ORF11 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 20: 2 ORF14 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 21: 2 ORF18 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 22: 2 ORF22 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 23: 2 ORF23 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 24: 2 ORF24 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 25: 2 ORF25 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 26: 2 ORF26 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 27: 2 ORF28 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 28: 2 ORF29 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 29: 2 ORF33 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 30: 2 ORF35.5 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 31: 2 ORF36 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 32: 2 ORF39 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 33: 2 CTO 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 34: 2 ORF40 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 35: 2 ORF42 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 36: 2 ORF43 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 37: 2 ORF44 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 38: 2 ORF46 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 39: 2 ORF58 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 40: 2 ORF62 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 41: 2 ORF66_1 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 42: 2 ORF68 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 43: 2 ORF73 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 44: 2 ORF74 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 45: 2 ORF75 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 46: 2 ORF76 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 47: 3 ORF5 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 48: 3 ORF7 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 49: 3 ORF10 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 50: 3 ORF17 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 51: 3 ORF30 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 52: 3 ORF53 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 53: 3 ORF63 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 54: 3 NOIR_2 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 55: 4 ORF6 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 56: 4 ORF65_1 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 57: 4 ORF67_1 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 58: 5 ORF12 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 59: 5 ORF13 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 60: 5 ORF15 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 61: 5 ORF16 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 62: 5 ORF27 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 63: 5 ORF32 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 64: 5 ORF35 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 65: 5 ORF41 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 66: 5 ORF48 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 67: 5 ORF52 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 68: 5 ORF54 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 69: 5 ORF57 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 70: 5 ORF59 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 71: 5 ORF60 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 72: 5 NOIR_1 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 73: 5 ORF71 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 74: 5 ORF72 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 75: 6 ORF69 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 76: 6 ORF70 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.002462135 -2.7431302 0.9996434 0.111936808
## 2: 0.002462135 -2.7431302 0.9996434 0.111936808
## 3: 0.002462135 -2.7431302 0.9996434 0.111936808
## 4: 0.002462135 -2.7431302 0.9996434 0.111936808
## 5: 0.002462135 -2.7431302 0.9996434 0.111936808
## 6: 0.002462135 -2.7431302 0.9996434 0.111936808
## 7: 0.002462135 -2.7431302 0.9996434 0.111936808
## 8: 0.002462135 -2.7431302 0.9996434 0.111936808
## 9: 0.002462135 -2.7431302 0.9996434 0.111936808
## 10: 0.002462135 -2.7431302 0.9996434 0.111936808
## 11: 0.002462135 -2.7431302 0.9996434 0.111936808
## 12: 0.002462135 -2.7431302 0.9996434 0.111936808
## 13: 0.002462135 -2.7431302 0.9996434 0.111936808
## 14: 0.002462135 -2.7431302 0.9996434 0.111936808
## 15: 0.002462135 -2.7431302 0.9996434 0.111936808
## 16: 0.004791635 -1.4740665 0.8338440 0.032372715
## 17: 0.004791635 -1.4740665 0.8338440 0.032372715
## 18: 0.004791635 -1.4740665 0.8338440 0.032372715
## 19: 0.004791635 -1.4740665 0.8338440 0.032372715
## 20: 0.004791635 -1.4740665 0.8338440 0.032372715
## 21: 0.004791635 -1.4740665 0.8338440 0.032372715
## 22: 0.004791635 -1.4740665 0.8338440 0.032372715
## 23: 0.004791635 -1.4740665 0.8338440 0.032372715
## 24: 0.004791635 -1.4740665 0.8338440 0.032372715
## 25: 0.004791635 -1.4740665 0.8338440 0.032372715
## 26: 0.004791635 -1.4740665 0.8338440 0.032372715
## 27: 0.004791635 -1.4740665 0.8338440 0.032372715
## 28: 0.004791635 -1.4740665 0.8338440 0.032372715
## 29: 0.004791635 -1.4740665 0.8338440 0.032372715
## 30: 0.004791635 -1.4740665 0.8338440 0.032372715
## 31: 0.004791635 -1.4740665 0.8338440 0.032372715
## 32: 0.004791635 -1.4740665 0.8338440 0.032372715
## 33: 0.004791635 -1.4740665 0.8338440 0.032372715
## 34: 0.004791635 -1.4740665 0.8338440 0.032372715
## 35: 0.004791635 -1.4740665 0.8338440 0.032372715
## 36: 0.004791635 -1.4740665 0.8338440 0.032372715
## 37: 0.004791635 -1.4740665 0.8338440 0.032372715
## 38: 0.004791635 -1.4740665 0.8338440 0.032372715
## 39: 0.004791635 -1.4740665 0.8338440 0.032372715
## 40: 0.004791635 -1.4740665 0.8338440 0.032372715
## 41: 0.004791635 -1.4740665 0.8338440 0.032372715
## 42: 0.004791635 -1.4740665 0.8338440 0.032372715
## 43: 0.004791635 -1.4740665 0.8338440 0.032372715
## 44: 0.004791635 -1.4740665 0.8338440 0.032372715
## 45: 0.004791635 -1.4740665 0.8338440 0.032372715
## 46: 0.004791635 -1.4740665 0.8338440 0.032372715
## 47: 0.003807918 -2.3395432 1.1685483 0.376504068
## 48: 0.003807918 -2.3395432 1.1685483 0.376504068
## 49: 0.003807918 -2.3395432 1.1685483 0.376504068
## 50: 0.003807918 -2.3395432 1.1685483 0.376504068
## 51: 0.003807918 -2.3395432 1.1685483 0.376504068
## 52: 0.003807918 -2.3395432 1.1685483 0.376504068
## 53: 0.003807918 -2.3395432 1.1685483 0.376504068
## 54: 0.003807918 -2.3395432 1.1685483 0.376504068
## 55: 0.004535461 -1.6400338 0.8477994 0.110459671
## 56: 0.004535461 -1.6400338 0.8477994 0.110459671
## 57: 0.004535461 -1.6400338 0.8477994 0.110459671
## 58: 0.005045937 -0.7647494 0.3581624 0.003891377
## 59: 0.005045937 -0.7647494 0.3581624 0.003891377
## 60: 0.005045937 -0.7647494 0.3581624 0.003891377
## 61: 0.005045937 -0.7647494 0.3581624 0.003891377
## 62: 0.005045937 -0.7647494 0.3581624 0.003891377
## 63: 0.005045937 -0.7647494 0.3581624 0.003891377
## 64: 0.005045937 -0.7647494 0.3581624 0.003891377
## 65: 0.005045937 -0.7647494 0.3581624 0.003891377
## 66: 0.005045937 -0.7647494 0.3581624 0.003891377
## 67: 0.005045937 -0.7647494 0.3581624 0.003891377
## 68: 0.005045937 -0.7647494 0.3581624 0.003891377
## 69: 0.005045937 -0.7647494 0.3581624 0.003891377
## 70: 0.005045937 -0.7647494 0.3581624 0.003891377
## 71: 0.005045937 -0.7647494 0.3581624 0.003891377
## 72: 0.005045937 -0.7647494 0.3581624 0.003891377
## 73: 0.005045937 -0.7647494 0.3581624 0.003891377
## 74: 0.005045937 -0.7647494 0.3581624 0.003891377
## 75: 0.005360081 -1.2259504 1.2355113 0.836797742
## 76: 0.005360081 -1.2259504 1.2355113 0.836797742
## se.bp v c pchi
## [1] "ORF61" "ORF21" "ORF49" "ORF19" "ORF31" "ORF1" "ORF62" "ORF18"
## [9] "ORF32" "ORF59" "NOIR_1" "ORF69"## [1] 12## [1] "ORF12" "ORF13" "ORF15" "ORF16" "ORF27" "ORF32" "ORF35" "ORF41"
## [9] "ORF48" "ORF52" "ORF54" "ORF57" "ORF59" "ORF60" "NOIR_1" "ORF71"
## [17] "ORF72"## [1] 17Clustering statistics: Cluster number: 7
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 2: 1 ORF4 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 3: 1 ORF9 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 4: 1 ORF19 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 5: 1 ORF20 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 6: 1 ORF21 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 7: 1 ORF31 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 8: 1 ORF34 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 9: 1 ORF37 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 10: 1 ORF38 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 11: 1 ORF49 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 12: 1 ORF50 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 13: 1 ORF51 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 14: 1 ORF61 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 15: 1 ORF64_1 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 16: 2 ORF2 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 17: 2 ORF3 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 18: 2 ORF8 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 19: 2 ORF11 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 20: 2 ORF14 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 21: 2 ORF18 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 22: 2 ORF22 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 23: 2 ORF23 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 24: 2 ORF24 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 25: 2 ORF25 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 26: 2 ORF26 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 27: 2 ORF28 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 28: 2 ORF29 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 29: 2 ORF33 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 30: 2 ORF35.5 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 31: 2 ORF36 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 32: 2 ORF39 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 33: 2 CTO 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 34: 2 ORF40 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 35: 2 ORF42 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 36: 2 ORF43 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 37: 2 ORF44 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 38: 2 ORF46 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 39: 2 ORF58 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 40: 2 ORF62 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 41: 2 ORF66_1 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 42: 2 ORF68 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 43: 2 ORF73 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 44: 2 ORF74 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 45: 2 ORF75 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 46: 2 ORF76 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 47: 3 ORF5 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 48: 3 ORF7 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 49: 3 ORF10 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 50: 3 ORF17 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 51: 3 ORF30 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 52: 3 ORF53 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 53: 3 ORF63 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 54: 3 NOIR_2 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 55: 4 ORF6 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 56: 4 ORF65_1 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 57: 4 ORF67_1 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 58: 5 ORF12 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 59: 5 ORF13 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 60: 5 ORF15 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 61: 5 ORF16 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 62: 5 ORF35 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 63: 5 ORF41 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 64: 5 ORF48 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 65: 5 ORF52 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 66: 5 ORF54 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 67: 5 ORF57 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 68: 5 ORF60 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 69: 5 ORF71 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 70: 5 ORF72 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 71: 6 ORF27 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 72: 6 ORF32 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 73: 6 ORF59 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 74: 6 NOIR_1 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 75: 7 ORF69 0.9950502 0.9993827 0.8231197 0.0012200616 1.928466e-04
## 76: 7 ORF70 0.9950502 0.9993827 0.8231197 0.0012200616 1.928466e-04
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.002462135 -2.7431302 0.9996434 0.111936808
## 2: 0.002462135 -2.7431302 0.9996434 0.111936808
## 3: 0.002462135 -2.7431302 0.9996434 0.111936808
## 4: 0.002462135 -2.7431302 0.9996434 0.111936808
## 5: 0.002462135 -2.7431302 0.9996434 0.111936808
## 6: 0.002462135 -2.7431302 0.9996434 0.111936808
## 7: 0.002462135 -2.7431302 0.9996434 0.111936808
## 8: 0.002462135 -2.7431302 0.9996434 0.111936808
## 9: 0.002462135 -2.7431302 0.9996434 0.111936808
## 10: 0.002462135 -2.7431302 0.9996434 0.111936808
## 11: 0.002462135 -2.7431302 0.9996434 0.111936808
## 12: 0.002462135 -2.7431302 0.9996434 0.111936808
## 13: 0.002462135 -2.7431302 0.9996434 0.111936808
## 14: 0.002462135 -2.7431302 0.9996434 0.111936808
## 15: 0.002462135 -2.7431302 0.9996434 0.111936808
## 16: 0.004791635 -1.4740665 0.8338440 0.032372715
## 17: 0.004791635 -1.4740665 0.8338440 0.032372715
## 18: 0.004791635 -1.4740665 0.8338440 0.032372715
## 19: 0.004791635 -1.4740665 0.8338440 0.032372715
## 20: 0.004791635 -1.4740665 0.8338440 0.032372715
## 21: 0.004791635 -1.4740665 0.8338440 0.032372715
## 22: 0.004791635 -1.4740665 0.8338440 0.032372715
## 23: 0.004791635 -1.4740665 0.8338440 0.032372715
## 24: 0.004791635 -1.4740665 0.8338440 0.032372715
## 25: 0.004791635 -1.4740665 0.8338440 0.032372715
## 26: 0.004791635 -1.4740665 0.8338440 0.032372715
## 27: 0.004791635 -1.4740665 0.8338440 0.032372715
## 28: 0.004791635 -1.4740665 0.8338440 0.032372715
## 29: 0.004791635 -1.4740665 0.8338440 0.032372715
## 30: 0.004791635 -1.4740665 0.8338440 0.032372715
## 31: 0.004791635 -1.4740665 0.8338440 0.032372715
## 32: 0.004791635 -1.4740665 0.8338440 0.032372715
## 33: 0.004791635 -1.4740665 0.8338440 0.032372715
## 34: 0.004791635 -1.4740665 0.8338440 0.032372715
## 35: 0.004791635 -1.4740665 0.8338440 0.032372715
## 36: 0.004791635 -1.4740665 0.8338440 0.032372715
## 37: 0.004791635 -1.4740665 0.8338440 0.032372715
## 38: 0.004791635 -1.4740665 0.8338440 0.032372715
## 39: 0.004791635 -1.4740665 0.8338440 0.032372715
## 40: 0.004791635 -1.4740665 0.8338440 0.032372715
## 41: 0.004791635 -1.4740665 0.8338440 0.032372715
## 42: 0.004791635 -1.4740665 0.8338440 0.032372715
## 43: 0.004791635 -1.4740665 0.8338440 0.032372715
## 44: 0.004791635 -1.4740665 0.8338440 0.032372715
## 45: 0.004791635 -1.4740665 0.8338440 0.032372715
## 46: 0.004791635 -1.4740665 0.8338440 0.032372715
## 47: 0.003807918 -2.3395432 1.1685483 0.376504068
## 48: 0.003807918 -2.3395432 1.1685483 0.376504068
## 49: 0.003807918 -2.3395432 1.1685483 0.376504068
## 50: 0.003807918 -2.3395432 1.1685483 0.376504068
## 51: 0.003807918 -2.3395432 1.1685483 0.376504068
## 52: 0.003807918 -2.3395432 1.1685483 0.376504068
## 53: 0.003807918 -2.3395432 1.1685483 0.376504068
## 54: 0.003807918 -2.3395432 1.1685483 0.376504068
## 55: 0.004535461 -1.6400338 0.8477994 0.110459671
## 56: 0.004535461 -1.6400338 0.8477994 0.110459671
## 57: 0.004535461 -1.6400338 0.8477994 0.110459671
## 58: 0.005045937 -0.7647494 0.3581624 0.003891377
## 59: 0.005045937 -0.7647494 0.3581624 0.003891377
## 60: 0.005045937 -0.7647494 0.3581624 0.003891377
## 61: 0.005045937 -0.7647494 0.3581624 0.003891377
## 62: 0.005045937 -0.7647494 0.3581624 0.003891377
## 63: 0.005045937 -0.7647494 0.3581624 0.003891377
## 64: 0.005045937 -0.7647494 0.3581624 0.003891377
## 65: 0.005045937 -0.7647494 0.3581624 0.003891377
## 66: 0.005045937 -0.7647494 0.3581624 0.003891377
## 67: 0.005045937 -0.7647494 0.3581624 0.003891377
## 68: 0.005045937 -0.7647494 0.3581624 0.003891377
## 69: 0.005045937 -0.7647494 0.3581624 0.003891377
## 70: 0.005045937 -0.7647494 0.3581624 0.003891377
## 71: 0.005360081 -1.2259504 1.2355113 0.836797742
## 72: 0.005360081 -1.2259504 1.2355113 0.836797742
## 73: 0.005360081 -1.2259504 1.2355113 0.836797742
## 74: 0.005360081 -1.2259504 1.2355113 0.836797742
## 75: 0.004345545 -2.0790323 1.1517128 0.463550040
## 76: 0.004345545 -2.0790323 1.1517128 0.463550040
## se.bp v c pchi
## [1] "ORF61" "ORF21" "ORF49" "ORF19" "ORF31" "ORF1" "ORF18" "ORF42" "ORF33"
## [10] "ORF62" "ORF69"## [1] 11## [1] "ORF12" "ORF13" "ORF15" "ORF16" "ORF35" "ORF41" "ORF48" "ORF52" "ORF54"
## [10] "ORF57" "ORF60" "ORF71" "ORF72"## [1] 13Clustering statistics: Cluster number: 10
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 2: 1 ORF4 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 3: 1 ORF9 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 4: 1 ORF20 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 5: 1 ORF21 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 6: 1 ORF31 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 7: 1 ORF34 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 8: 1 ORF38 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 9: 1 ORF50 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 10: 1 ORF61 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 11: 1 ORF64_1 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 12: 2 ORF2 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 13: 2 ORF3 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 14: 2 ORF11 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 15: 2 ORF14 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 16: 2 ORF18 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 17: 2 ORF26 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 18: 2 ORF28 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 19: 2 ORF29 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 20: 2 ORF39 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 21: 2 ORF40 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 22: 2 ORF66_1 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 23: 2 ORF68 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 24: 2 ORF73 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 25: 2 ORF75 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 26: 2 ORF76 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 27: 3 ORF5 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 28: 3 ORF7 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 29: 3 ORF10 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 30: 3 ORF17 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 31: 3 ORF30 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 32: 3 ORF53 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 33: 3 ORF63 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 34: 3 NOIR_2 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 35: 4 ORF6 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 36: 4 ORF65_1 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 37: 4 ORF67_1 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 38: 5 ORF8 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 39: 5 ORF22 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 40: 5 ORF23 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 41: 5 ORF25 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 42: 5 ORF33 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 43: 5 ORF35.5 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 44: 5 ORF36 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 45: 5 CTO 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 46: 5 ORF42 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 47: 5 ORF43 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 48: 5 ORF44 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 49: 5 ORF46 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 50: 5 ORF58 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 51: 5 ORF62 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 52: 6 ORF12 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 53: 6 ORF13 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 54: 6 ORF15 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 55: 6 ORF16 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 56: 6 ORF35 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 57: 6 ORF41 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 58: 6 ORF48 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 59: 6 ORF52 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 60: 6 ORF54 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 61: 6 ORF57 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 62: 6 ORF60 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 63: 6 ORF71 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 64: 6 ORF72 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 65: 7 ORF19 0.9950502 0.9993827 0.8231197 0.0012200616 1.928466e-04
## 66: 7 ORF37 0.9950502 0.9993827 0.8231197 0.0012200616 1.928466e-04
## 67: 7 ORF49 0.9950502 0.9993827 0.8231197 0.0012200616 1.928466e-04
## 68: 7 ORF51 0.9950502 0.9993827 0.8231197 0.0012200616 1.928466e-04
## 69: 8 ORF24 0.8269550 0.9600770 0.6097052 0.0209797534 6.760864e-03
## 70: 8 ORF74 0.8269550 0.9600770 0.6097052 0.0209797534 6.760864e-03
## 71: 9 ORF27 0.3644979 0.8395897 0.3665347 0.0472966570 1.959926e-02
## 72: 9 ORF32 0.3644979 0.8395897 0.3665347 0.0472966570 1.959926e-02
## 73: 9 ORF59 0.3644979 0.8395897 0.3665347 0.0472966570 1.959926e-02
## 74: 9 NOIR_1 0.3644979 0.8395897 0.3665347 0.0472966570 1.959926e-02
## 75: 10 ORF69 0.9889970 0.9986601 0.7485506 0.0023411578 3.704194e-04
## 76: 10 ORF70 0.9889970 0.9986601 0.7485506 0.0023411578 3.704194e-04
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.002462135 -2.7431302 0.9996434 0.111936808
## 2: 0.002462135 -2.7431302 0.9996434 0.111936808
## 3: 0.002462135 -2.7431302 0.9996434 0.111936808
## 4: 0.002462135 -2.7431302 0.9996434 0.111936808
## 5: 0.002462135 -2.7431302 0.9996434 0.111936808
## 6: 0.002462135 -2.7431302 0.9996434 0.111936808
## 7: 0.002462135 -2.7431302 0.9996434 0.111936808
## 8: 0.002462135 -2.7431302 0.9996434 0.111936808
## 9: 0.002462135 -2.7431302 0.9996434 0.111936808
## 10: 0.002462135 -2.7431302 0.9996434 0.111936808
## 11: 0.002462135 -2.7431302 0.9996434 0.111936808
## 12: 0.004791635 -1.4740665 0.8338440 0.032372715
## 13: 0.004791635 -1.4740665 0.8338440 0.032372715
## 14: 0.004791635 -1.4740665 0.8338440 0.032372715
## 15: 0.004791635 -1.4740665 0.8338440 0.032372715
## 16: 0.004791635 -1.4740665 0.8338440 0.032372715
## 17: 0.004791635 -1.4740665 0.8338440 0.032372715
## 18: 0.004791635 -1.4740665 0.8338440 0.032372715
## 19: 0.004791635 -1.4740665 0.8338440 0.032372715
## 20: 0.004791635 -1.4740665 0.8338440 0.032372715
## 21: 0.004791635 -1.4740665 0.8338440 0.032372715
## 22: 0.004791635 -1.4740665 0.8338440 0.032372715
## 23: 0.004791635 -1.4740665 0.8338440 0.032372715
## 24: 0.004791635 -1.4740665 0.8338440 0.032372715
## 25: 0.004791635 -1.4740665 0.8338440 0.032372715
## 26: 0.004791635 -1.4740665 0.8338440 0.032372715
## 27: 0.003807918 -2.3395432 1.1685483 0.376504068
## 28: 0.003807918 -2.3395432 1.1685483 0.376504068
## 29: 0.003807918 -2.3395432 1.1685483 0.376504068
## 30: 0.003807918 -2.3395432 1.1685483 0.376504068
## 31: 0.003807918 -2.3395432 1.1685483 0.376504068
## 32: 0.003807918 -2.3395432 1.1685483 0.376504068
## 33: 0.003807918 -2.3395432 1.1685483 0.376504068
## 34: 0.003807918 -2.3395432 1.1685483 0.376504068
## 35: 0.004535461 -1.6400338 0.8477994 0.110459671
## 36: 0.004535461 -1.6400338 0.8477994 0.110459671
## 37: 0.004535461 -1.6400338 0.8477994 0.110459671
## 38: 0.005045937 -0.7647494 0.3581624 0.003891377
## 39: 0.005045937 -0.7647494 0.3581624 0.003891377
## 40: 0.005045937 -0.7647494 0.3581624 0.003891377
## 41: 0.005045937 -0.7647494 0.3581624 0.003891377
## 42: 0.005045937 -0.7647494 0.3581624 0.003891377
## 43: 0.005045937 -0.7647494 0.3581624 0.003891377
## 44: 0.005045937 -0.7647494 0.3581624 0.003891377
## 45: 0.005045937 -0.7647494 0.3581624 0.003891377
## 46: 0.005045937 -0.7647494 0.3581624 0.003891377
## 47: 0.005045937 -0.7647494 0.3581624 0.003891377
## 48: 0.005045937 -0.7647494 0.3581624 0.003891377
## 49: 0.005045937 -0.7647494 0.3581624 0.003891377
## 50: 0.005045937 -0.7647494 0.3581624 0.003891377
## 51: 0.005045937 -0.7647494 0.3581624 0.003891377
## 52: 0.005360081 -1.2259504 1.2355113 0.836797742
## 53: 0.005360081 -1.2259504 1.2355113 0.836797742
## 54: 0.005360081 -1.2259504 1.2355113 0.836797742
## 55: 0.005360081 -1.2259504 1.2355113 0.836797742
## 56: 0.005360081 -1.2259504 1.2355113 0.836797742
## 57: 0.005360081 -1.2259504 1.2355113 0.836797742
## 58: 0.005360081 -1.2259504 1.2355113 0.836797742
## 59: 0.005360081 -1.2259504 1.2355113 0.836797742
## 60: 0.005360081 -1.2259504 1.2355113 0.836797742
## 61: 0.005360081 -1.2259504 1.2355113 0.836797742
## 62: 0.005360081 -1.2259504 1.2355113 0.836797742
## 63: 0.005360081 -1.2259504 1.2355113 0.836797742
## 64: 0.005360081 -1.2259504 1.2355113 0.836797742
## 65: 0.004345545 -2.0790323 1.1517128 0.463550040
## 66: 0.004345545 -2.0790323 1.1517128 0.463550040
## 67: 0.004345545 -2.0790323 1.1517128 0.463550040
## 68: 0.004345545 -2.0790323 1.1517128 0.463550040
## 69: 0.005225604 -1.0150655 0.7365148 0.581381554
## 70: 0.005225604 -1.0150655 0.7365148 0.581381554
## 71: 0.005072069 -0.3258638 0.6669091 0.971154607
## 72: 0.005072069 -0.3258638 0.6669091 0.971154607
## 73: 0.005072069 -0.3258638 0.6669091 0.971154607
## 74: 0.005072069 -0.3258638 0.6669091 0.971154607
## 75: 0.004828418 -1.8361023 1.1661667 0.514478070
## 76: 0.004828418 -1.8361023 1.1661667 0.514478070
## se.bp v c pchi
## [1] "ORF1" "ORF68" "ORF36" "ORF19" "ORF49" "ORF59" "ORF69"## [1] 7## [1] "ORF8" "ORF22" "ORF23" "ORF25" "ORF33" "ORF35.5" "ORF36"
## [8] "CTO" "ORF42" "ORF43" "ORF44" "ORF46" "ORF58" "ORF62"
## [15] "ORF27" "ORF32" "ORF59" "NOIR_1"## [1] 18Clustering statistics: Cluster number: 12
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 2: 1 ORF4 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 3: 1 ORF9 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 4: 1 ORF20 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 5: 1 ORF21 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 6: 1 ORF31 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 7: 1 ORF34 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 8: 1 ORF38 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 9: 1 ORF50 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 10: 1 ORF61 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 11: 2 ORF2 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 12: 2 ORF3 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 13: 2 ORF11 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 14: 2 ORF14 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 15: 2 ORF18 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 16: 2 ORF26 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 17: 2 ORF28 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 18: 2 ORF29 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 19: 2 ORF39 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 20: 2 ORF40 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 21: 2 ORF66_1 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 22: 2 ORF68 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 23: 2 ORF73 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 24: 2 ORF75 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 25: 2 ORF76 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 26: 3 ORF5 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 27: 3 ORF7 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 28: 3 ORF10 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 29: 3 ORF17 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 30: 3 ORF30 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 31: 3 ORF53 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 32: 3 ORF63 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 33: 3 NOIR_2 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 34: 4 ORF6 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 35: 4 ORF65_1 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 36: 4 ORF67_1 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 37: 5 ORF8 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 38: 5 ORF22 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 39: 5 ORF23 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 40: 5 ORF25 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 41: 5 ORF33 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 42: 5 ORF35.5 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 43: 5 ORF36 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 44: 5 CTO 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 45: 5 ORF42 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 46: 5 ORF43 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 47: 5 ORF44 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 48: 5 ORF46 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 49: 5 ORF58 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 50: 5 ORF62 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 51: 6 ORF12 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 52: 6 ORF13 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 53: 6 ORF15 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 54: 6 ORF16 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 55: 6 ORF35 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 56: 6 ORF41 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 57: 6 ORF48 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 58: 6 ORF52 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 59: 6 ORF54 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 60: 6 ORF57 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 61: 6 ORF60 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 62: 6 ORF71 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 63: 6 ORF72 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 64: 7 ORF19 0.9950502 0.9993827 0.8231197 0.0012200616 1.928466e-04
## 65: 7 ORF37 0.9950502 0.9993827 0.8231197 0.0012200616 1.928466e-04
## 66: 7 ORF49 0.9950502 0.9993827 0.8231197 0.0012200616 1.928466e-04
## 67: 7 ORF51 0.9950502 0.9993827 0.8231197 0.0012200616 1.928466e-04
## 68: 8 ORF24 0.8269550 0.9600770 0.6097052 0.0209797534 6.760864e-03
## 69: 8 ORF74 0.8269550 0.9600770 0.6097052 0.0209797534 6.760864e-03
## 70: 9 ORF27 0.3644979 0.8395897 0.3665347 0.0472966570 1.959926e-02
## 71: 9 ORF32 0.3644979 0.8395897 0.3665347 0.0472966570 1.959926e-02
## 72: 9 ORF59 0.3644979 0.8395897 0.3665347 0.0472966570 1.959926e-02
## 73: 10 ORF64_1 0.9889970 0.9986601 0.7485506 0.0023411578 3.704194e-04
## 74: 11 NOIR_1 0.9931468 0.9991447 0.7977848 0.0015928803 2.541478e-04
## 75: 12 ORF69 0.5739085 0.9370812 0.2869637 0.0454648819 1.080970e-02
## 76: 12 ORF70 0.5739085 0.9370812 0.2869637 0.0454648819 1.080970e-02
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.002462135 -2.7431302 0.9996434 0.111936808
## 2: 0.002462135 -2.7431302 0.9996434 0.111936808
## 3: 0.002462135 -2.7431302 0.9996434 0.111936808
## 4: 0.002462135 -2.7431302 0.9996434 0.111936808
## 5: 0.002462135 -2.7431302 0.9996434 0.111936808
## 6: 0.002462135 -2.7431302 0.9996434 0.111936808
## 7: 0.002462135 -2.7431302 0.9996434 0.111936808
## 8: 0.002462135 -2.7431302 0.9996434 0.111936808
## 9: 0.002462135 -2.7431302 0.9996434 0.111936808
## 10: 0.002462135 -2.7431302 0.9996434 0.111936808
## 11: 0.004791635 -1.4740665 0.8338440 0.032372715
## 12: 0.004791635 -1.4740665 0.8338440 0.032372715
## 13: 0.004791635 -1.4740665 0.8338440 0.032372715
## 14: 0.004791635 -1.4740665 0.8338440 0.032372715
## 15: 0.004791635 -1.4740665 0.8338440 0.032372715
## 16: 0.004791635 -1.4740665 0.8338440 0.032372715
## 17: 0.004791635 -1.4740665 0.8338440 0.032372715
## 18: 0.004791635 -1.4740665 0.8338440 0.032372715
## 19: 0.004791635 -1.4740665 0.8338440 0.032372715
## 20: 0.004791635 -1.4740665 0.8338440 0.032372715
## 21: 0.004791635 -1.4740665 0.8338440 0.032372715
## 22: 0.004791635 -1.4740665 0.8338440 0.032372715
## 23: 0.004791635 -1.4740665 0.8338440 0.032372715
## 24: 0.004791635 -1.4740665 0.8338440 0.032372715
## 25: 0.004791635 -1.4740665 0.8338440 0.032372715
## 26: 0.003807918 -2.3395432 1.1685483 0.376504068
## 27: 0.003807918 -2.3395432 1.1685483 0.376504068
## 28: 0.003807918 -2.3395432 1.1685483 0.376504068
## 29: 0.003807918 -2.3395432 1.1685483 0.376504068
## 30: 0.003807918 -2.3395432 1.1685483 0.376504068
## 31: 0.003807918 -2.3395432 1.1685483 0.376504068
## 32: 0.003807918 -2.3395432 1.1685483 0.376504068
## 33: 0.003807918 -2.3395432 1.1685483 0.376504068
## 34: 0.004535461 -1.6400338 0.8477994 0.110459671
## 35: 0.004535461 -1.6400338 0.8477994 0.110459671
## 36: 0.004535461 -1.6400338 0.8477994 0.110459671
## 37: 0.005045937 -0.7647494 0.3581624 0.003891377
## 38: 0.005045937 -0.7647494 0.3581624 0.003891377
## 39: 0.005045937 -0.7647494 0.3581624 0.003891377
## 40: 0.005045937 -0.7647494 0.3581624 0.003891377
## 41: 0.005045937 -0.7647494 0.3581624 0.003891377
## 42: 0.005045937 -0.7647494 0.3581624 0.003891377
## 43: 0.005045937 -0.7647494 0.3581624 0.003891377
## 44: 0.005045937 -0.7647494 0.3581624 0.003891377
## 45: 0.005045937 -0.7647494 0.3581624 0.003891377
## 46: 0.005045937 -0.7647494 0.3581624 0.003891377
## 47: 0.005045937 -0.7647494 0.3581624 0.003891377
## 48: 0.005045937 -0.7647494 0.3581624 0.003891377
## 49: 0.005045937 -0.7647494 0.3581624 0.003891377
## 50: 0.005045937 -0.7647494 0.3581624 0.003891377
## 51: 0.005360081 -1.2259504 1.2355113 0.836797742
## 52: 0.005360081 -1.2259504 1.2355113 0.836797742
## 53: 0.005360081 -1.2259504 1.2355113 0.836797742
## 54: 0.005360081 -1.2259504 1.2355113 0.836797742
## 55: 0.005360081 -1.2259504 1.2355113 0.836797742
## 56: 0.005360081 -1.2259504 1.2355113 0.836797742
## 57: 0.005360081 -1.2259504 1.2355113 0.836797742
## 58: 0.005360081 -1.2259504 1.2355113 0.836797742
## 59: 0.005360081 -1.2259504 1.2355113 0.836797742
## 60: 0.005360081 -1.2259504 1.2355113 0.836797742
## 61: 0.005360081 -1.2259504 1.2355113 0.836797742
## 62: 0.005360081 -1.2259504 1.2355113 0.836797742
## 63: 0.005360081 -1.2259504 1.2355113 0.836797742
## 64: 0.004345545 -2.0790323 1.1517128 0.463550040
## 65: 0.004345545 -2.0790323 1.1517128 0.463550040
## 66: 0.004345545 -2.0790323 1.1517128 0.463550040
## 67: 0.004345545 -2.0790323 1.1517128 0.463550040
## 68: 0.005225604 -1.0150655 0.7365148 0.581381554
## 69: 0.005225604 -1.0150655 0.7365148 0.581381554
## 70: 0.005072069 -0.3258638 0.6669091 0.971154607
## 71: 0.005072069 -0.3258638 0.6669091 0.971154607
## 72: 0.005072069 -0.3258638 0.6669091 0.971154607
## 73: 0.004828418 -1.8361023 1.1661667 0.514478070
## 74: 0.004537195 -1.9850487 1.1513140 0.203301269
## 75: 0.004755718 -0.4842235 1.0465005 0.269712204
## 76: 0.004755718 -0.4842235 1.0465005 0.269712204
## se.bp v c pchi
## [1] "ORF68" "ORF36" "ORF19" "ORF49" "ORF69"## [1] 5## [1] "ORF8" "ORF22" "ORF23" "ORF25" "ORF33" "ORF35.5" "ORF36"
## [8] "CTO" "ORF42" "ORF43" "ORF44" "ORF46" "ORF58" "ORF62"
## [15] "ORF27" "ORF32" "ORF59" "ORF69" "ORF70"## [1] 19Selected number of clusters: 12
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 2: 1 ORF4 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 3: 1 ORF9 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 4: 1 ORF20 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 5: 1 ORF21 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 6: 1 ORF31 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 7: 1 ORF34 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 8: 1 ORF38 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 9: 1 ORF50 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 10: 1 ORF61 0.9994267 0.9999090 0.9593757 0.0002469015 4.664129e-05
## 11: 2 ORF2 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 12: 2 ORF3 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 13: 2 ORF11 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 14: 2 ORF14 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 15: 2 ORF18 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 16: 2 ORF26 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 17: 2 ORF28 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 18: 2 ORF29 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 19: 2 ORF39 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 20: 2 ORF40 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 21: 2 ORF66_1 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 22: 2 ORF68 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 23: 2 ORF73 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 24: 2 ORF75 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 25: 2 ORF76 0.9480570 0.9894979 0.7389860 0.0085539492 2.278605e-03
## 26: 3 ORF5 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 27: 3 ORF7 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 28: 3 ORF10 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 29: 3 ORF17 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 30: 3 ORF30 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 31: 3 ORF53 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 32: 3 ORF63 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 33: 3 NOIR_2 0.9981395 0.9997743 0.8791996 0.0005447895 8.199212e-05
## 34: 4 ORF6 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 35: 4 ORF65_1 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 36: 4 ORF67_1 0.9675894 0.9935738 0.7858880 0.0059634129 1.528880e-03
## 37: 5 ORF8 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 38: 5 ORF22 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 39: 5 ORF23 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 40: 5 ORF25 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 41: 5 ORF33 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 42: 5 ORF35.5 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 43: 5 ORF36 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 44: 5 CTO 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 45: 5 ORF42 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 46: 5 ORF43 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 47: 5 ORF44 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 48: 5 ORF46 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 49: 5 ORF58 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 50: 5 ORF62 0.6369522 0.8692625 0.6578444 0.0324830224 1.662449e-02
## 51: 6 ORF12 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 52: 6 ORF13 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 53: 6 ORF15 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 54: 6 ORF16 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 55: 6 ORF35 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 56: 6 ORF41 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 57: 6 ORF48 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 58: 6 ORF52 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 59: 6 ORF54 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 60: 6 ORF57 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 61: 6 ORF60 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 62: 6 ORF71 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 63: 6 ORF72 0.9361281 0.9930814 0.4961858 0.0103410191 1.579236e-03
## 64: 7 ORF19 0.9950502 0.9993827 0.8231197 0.0012200616 1.928466e-04
## 65: 7 ORF37 0.9950502 0.9993827 0.8231197 0.0012200616 1.928466e-04
## 66: 7 ORF49 0.9950502 0.9993827 0.8231197 0.0012200616 1.928466e-04
## 67: 7 ORF51 0.9950502 0.9993827 0.8231197 0.0012200616 1.928466e-04
## 68: 8 ORF24 0.8269550 0.9600770 0.6097052 0.0209797534 6.760864e-03
## 69: 8 ORF74 0.8269550 0.9600770 0.6097052 0.0209797534 6.760864e-03
## 70: 9 ORF27 0.3644979 0.8395897 0.3665347 0.0472966570 1.959926e-02
## 71: 9 ORF32 0.3644979 0.8395897 0.3665347 0.0472966570 1.959926e-02
## 72: 9 ORF59 0.3644979 0.8395897 0.3665347 0.0472966570 1.959926e-02
## 73: 10 ORF64_1 0.9889970 0.9986601 0.7485506 0.0023411578 3.704194e-04
## 74: 11 NOIR_1 0.9931468 0.9991447 0.7977848 0.0015928803 2.541478e-04
## 75: 12 ORF69 0.5739085 0.9370812 0.2869637 0.0454648819 1.080970e-02
## 76: 12 ORF70 0.5739085 0.9370812 0.2869637 0.0454648819 1.080970e-02
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.002462135 -2.7431302 0.9996434 0.111936808
## 2: 0.002462135 -2.7431302 0.9996434 0.111936808
## 3: 0.002462135 -2.7431302 0.9996434 0.111936808
## 4: 0.002462135 -2.7431302 0.9996434 0.111936808
## 5: 0.002462135 -2.7431302 0.9996434 0.111936808
## 6: 0.002462135 -2.7431302 0.9996434 0.111936808
## 7: 0.002462135 -2.7431302 0.9996434 0.111936808
## 8: 0.002462135 -2.7431302 0.9996434 0.111936808
## 9: 0.002462135 -2.7431302 0.9996434 0.111936808
## 10: 0.002462135 -2.7431302 0.9996434 0.111936808
## 11: 0.004791635 -1.4740665 0.8338440 0.032372715
## 12: 0.004791635 -1.4740665 0.8338440 0.032372715
## 13: 0.004791635 -1.4740665 0.8338440 0.032372715
## 14: 0.004791635 -1.4740665 0.8338440 0.032372715
## 15: 0.004791635 -1.4740665 0.8338440 0.032372715
## 16: 0.004791635 -1.4740665 0.8338440 0.032372715
## 17: 0.004791635 -1.4740665 0.8338440 0.032372715
## 18: 0.004791635 -1.4740665 0.8338440 0.032372715
## 19: 0.004791635 -1.4740665 0.8338440 0.032372715
## 20: 0.004791635 -1.4740665 0.8338440 0.032372715
## 21: 0.004791635 -1.4740665 0.8338440 0.032372715
## 22: 0.004791635 -1.4740665 0.8338440 0.032372715
## 23: 0.004791635 -1.4740665 0.8338440 0.032372715
## 24: 0.004791635 -1.4740665 0.8338440 0.032372715
## 25: 0.004791635 -1.4740665 0.8338440 0.032372715
## 26: 0.003807918 -2.3395432 1.1685483 0.376504068
## 27: 0.003807918 -2.3395432 1.1685483 0.376504068
## 28: 0.003807918 -2.3395432 1.1685483 0.376504068
## 29: 0.003807918 -2.3395432 1.1685483 0.376504068
## 30: 0.003807918 -2.3395432 1.1685483 0.376504068
## 31: 0.003807918 -2.3395432 1.1685483 0.376504068
## 32: 0.003807918 -2.3395432 1.1685483 0.376504068
## 33: 0.003807918 -2.3395432 1.1685483 0.376504068
## 34: 0.004535461 -1.6400338 0.8477994 0.110459671
## 35: 0.004535461 -1.6400338 0.8477994 0.110459671
## 36: 0.004535461 -1.6400338 0.8477994 0.110459671
## 37: 0.005045937 -0.7647494 0.3581624 0.003891377
## 38: 0.005045937 -0.7647494 0.3581624 0.003891377
## 39: 0.005045937 -0.7647494 0.3581624 0.003891377
## 40: 0.005045937 -0.7647494 0.3581624 0.003891377
## 41: 0.005045937 -0.7647494 0.3581624 0.003891377
## 42: 0.005045937 -0.7647494 0.3581624 0.003891377
## 43: 0.005045937 -0.7647494 0.3581624 0.003891377
## 44: 0.005045937 -0.7647494 0.3581624 0.003891377
## 45: 0.005045937 -0.7647494 0.3581624 0.003891377
## 46: 0.005045937 -0.7647494 0.3581624 0.003891377
## 47: 0.005045937 -0.7647494 0.3581624 0.003891377
## 48: 0.005045937 -0.7647494 0.3581624 0.003891377
## 49: 0.005045937 -0.7647494 0.3581624 0.003891377
## 50: 0.005045937 -0.7647494 0.3581624 0.003891377
## 51: 0.005360081 -1.2259504 1.2355113 0.836797742
## 52: 0.005360081 -1.2259504 1.2355113 0.836797742
## 53: 0.005360081 -1.2259504 1.2355113 0.836797742
## 54: 0.005360081 -1.2259504 1.2355113 0.836797742
## 55: 0.005360081 -1.2259504 1.2355113 0.836797742
## 56: 0.005360081 -1.2259504 1.2355113 0.836797742
## 57: 0.005360081 -1.2259504 1.2355113 0.836797742
## 58: 0.005360081 -1.2259504 1.2355113 0.836797742
## 59: 0.005360081 -1.2259504 1.2355113 0.836797742
## 60: 0.005360081 -1.2259504 1.2355113 0.836797742
## 61: 0.005360081 -1.2259504 1.2355113 0.836797742
## 62: 0.005360081 -1.2259504 1.2355113 0.836797742
## 63: 0.005360081 -1.2259504 1.2355113 0.836797742
## 64: 0.004345545 -2.0790323 1.1517128 0.463550040
## 65: 0.004345545 -2.0790323 1.1517128 0.463550040
## 66: 0.004345545 -2.0790323 1.1517128 0.463550040
## 67: 0.004345545 -2.0790323 1.1517128 0.463550040
## 68: 0.005225604 -1.0150655 0.7365148 0.581381554
## 69: 0.005225604 -1.0150655 0.7365148 0.581381554
## 70: 0.005072069 -0.3258638 0.6669091 0.971154607
## 71: 0.005072069 -0.3258638 0.6669091 0.971154607
## 72: 0.005072069 -0.3258638 0.6669091 0.971154607
## 73: 0.004828418 -1.8361023 1.1661667 0.514478070
## 74: 0.004537195 -1.9850487 1.1513140 0.203301269
## 75: 0.004755718 -0.4842235 1.0465005 0.269712204
## 76: 0.004755718 -0.4842235 1.0465005 0.269712204
## se.bp v c pchi
## [1] "ORF68" "ORF36" "ORF19" "ORF49" "ORF69"## [1] 5## [1] "ORF8" "ORF22" "ORF23" "ORF25" "ORF33" "ORF35.5" "ORF36"
## [8] "CTO" "ORF42" "ORF43" "ORF44" "ORF46" "ORF58" "ORF62"
## [15] "ORF27" "ORF32" "ORF59" "ORF69" "ORF70"## [1] 19Remove genes from clusters ?
## [1] "ORF8" "ORF22" "ORF23" "ORF25" "ORF33" "ORF35.5" "ORF36"
## [8] "CTO" "ORF42" "ORF43" "ORF44" "ORF46" "ORF58" "ORF62"
## [15] "ORF27" "ORF32" "ORF59" "ORF69" "ORF70"## [1] 19## No genes were removed from their corresponding clusters.## cluster N
## <int> <int>
## 1: 2 15
## 2: 5 14
## 3: 6 13
## 4: 1 10
## 5: 3 8
## 6: 7 4
## 7: 4 3
## 8: 9 3
## 9: 8 2
## 10: 12 2
## 11: 10 1
## 12: 11 1Merge cluster stats
Assigning genes to clusters
Summarize and melt
Heatmaps
Normalized Expression
Expression delta ~ 6 hpi
Z-score of expression delta ~ 6 hpi
ORF kinetics, according to literature-based kinetic classes
Barplot of mean and SD
Figure 4 REVIEW - Mean and SD with linear connection
Mean and SD with loess function
Mean and SD with linear connection - Figure 4
Each replicate with loess
ORF kinetics, according to de-novo kinetic classes
Mean and SD with linear connection
Figure 5 REVIEW - Mean and SD with linear connection
Compare literature and de novo kinetic classes
NA shows the number of genes where the clustering did not yield an unambiguous result.
Combined Kinetic classes
De Novo Clusters
Literature clusters
